Variant report

Variant	rs541993
Chromosome Location	chr11:75305557-75305558
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:75274194..75275717-chr11:75305204..75308053,2	K562	blood:
2	chr11:75301994..75305996-chr11:75306128..75308913,4	MCF-7	breast:
3	chr11:75303810..75306638-chr11:75313852..75316089,2	MCF-7	breast:
4	chr11:75294151..75295686-chr11:75303881..75305618,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SERPINH1-1	chr11:75305146-75305710	ENSG00000255326.1

Variant related genes	Relation type
ENSG00000255326	Chromatin interaction
ENSG00000149257	Chromatin interaction
ENSG00000255434	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1145696	0.91[CEU][hapmap];0.92[YRI][hapmap];0.92[EUR][1000 genomes]
rs1234668	0.92[EUR][1000 genomes]
rs2508193	0.90[EUR][1000 genomes]
rs4944086	0.82[TSI][hapmap]
rs544698	0.99[EUR][1000 genomes]
rs546156	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs590550	0.82[TSI][hapmap]
rs604694	0.91[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs641976	0.90[EUR][1000 genomes]
rs652452	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs654949	0.88[YRI][hapmap];0.90[EUR][1000 genomes]
rs656007	0.91[CEU][hapmap];0.80[GIH][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.90[EUR][1000 genomes]
rs657639	0.90[CEU][hapmap];0.83[YRI][hapmap];0.90[EUR][1000 genomes]
rs660343	0.91[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs663515	0.92[EUR][1000 genomes]
rs668378	0.90[EUR][1000 genomes]
rs687793	0.92[EUR][1000 genomes]
rs7110142	0.82[TSI][hapmap]
rs7114999	0.82[TSI][hapmap]
rs7128846	0.95[YRI][hapmap];0.90[EUR][1000 genomes]
rs7947980	0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3381903	chr11:75123498-75587233	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs541993	RAB6A	cis	cerebellum	SCAN
rs541993	NUMA1	cis	cerebellum	SCAN
rs541993	RELT	cis	cerebellum	SCAN
rs541993	KCTD21	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75295400-75329600	Weak transcription	Aorta	Aorta
2	chr11:75295600-75310800	Weak transcription	Right Atrium	heart
3	chr11:75295600-75314200	Weak transcription	Lung	lung
4	chr11:75295800-75316400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr11:75296600-75305800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:75296600-75321000	Weak transcription	Ovary	ovary
7	chr11:75301600-75313800	Weak transcription	Fetal Lung	lung
8	chr11:75302200-75306800	Enhancers	Fetal Muscle Leg	muscle
9	chr11:75302800-75312600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr11:75303600-75305800	Weak transcription	Fetal Thymus	thymus
11	chr11:75303600-75306000	Enhancers	Brain Hippocampus Middle	brain
12	chr11:75303800-75305600	Enhancers	Brain Angular Gyrus	brain
13	chr11:75303800-75305800	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr11:75303800-75306600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr11:75303800-75306800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr11:75303800-75307000	Enhancers	Brain Anterior Caudate	brain
17	chr11:75304000-75305800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr11:75304000-75305800	Enhancers	Brain Cingulate Gyrus	brain
19	chr11:75304000-75306000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr11:75304000-75306000	Enhancers	Brain Substantia Nigra	brain
21	chr11:75304000-75306200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr11:75304000-75306200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr11:75304000-75306400	Enhancers	Fetal Stomach	stomach
24	chr11:75304200-75305800	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr11:75304200-75306200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr11:75304400-75306600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr11:75304400-75306800	Enhancers	Brain Germinal Matrix	brain
28	chr11:75304600-75305600	Enhancers	Fetal Brain Female	brain
29	chr11:75304600-75306400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:75304800-75305600	Enhancers	Fetal Brain Male	brain
31	chr11:75304800-75306000	Weak transcription	Fetal Heart	heart
32	chr11:75304800-75306000	Enhancers	Rectal Smooth Muscle	rectum
33	chr11:75304800-75309200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:75305000-75307600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr11:75305000-75308800	Enhancers	K562	blood
36	chr11:75305000-75328800	Weak transcription	Pancreas	Pancrea
37	chr11:75305200-75306600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:75305200-75306600	Weak transcription	HSMMtube	muscle
39	chr11:75305200-75309400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr11:75305400-75305800	Weak transcription	Spleen	Spleen
41	chr11:75305400-75307800	Weak transcription	Fetal Intestine Small	intestine
42	chr11:75305400-75309000	Weak transcription	Fetal Intestine Large	intestine

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